As the show's fifth season ended, the X-Files had been shut down, and Mulder and Scully were assigned to other projects. The movie opens with them assisting Darius Michaud's FBI team staking out a building in Dallas which has had a bomb threat. They discover the bomb across the street but it explodes.

Through evidence given him by a paranoid doctor, Mulder grows to believe that the bomb was deliberately allowed to explode to destroy evidence of some victims of the alien virus. Despite the fact that he and Scully are in danger of losing their jobs at a hearing led by A.D. Jana Cassidy, and attended by A.D. Skinner, they pursue the evidence. But when Scully is stung by a bee infected with the virus, and is kidnapped, a desperate Mulder seeks her out. The Well-Manicured Man tells him where to find her, in Antarctica, and what the antidote is but in doing so, loses his life.

Mulder journeys to Antarctica and saves Scully, in the process discovering a secret lab run by the Cigarette-Smoking Man and his colleague Strughold. The lab is destroyed when the alien ship lying dormant comes back to life.

Later, Mulder and Scully give evidence at the hearing where Cassidy routinely ignores their remarks. At another outpost - in Tunisia - the Cigarette-Smoking Man learns that the X-Files office has been reopened...

The movie was actually filmed in the hiatus between the show's fourth and fifth seasons, and reshoots were done during the filming of the show's fifth season, which meant that some episodes of that season did not revolve around Mulder and/or Scully, because one or both actors were not available. Examples include "The Unusual Suspects," "Christmas Carol," "Chinga," and "Travelers."

The movie was responsible for introducing the show to a new group of fans. Many old fans of the show, however, believe that it reached its peak in the fourth or fifth season, and the movie was the beginning of the show's demise.

As is the case with many 20th Century Fox Films, the film cans for the advance screening prints and show prints had a code name. The X-Files was "Nuts and Bolts."

The working title "Blackwood" came from the works of English writer Algernon Blackwood (1869-1951), a member of the Golden Dawn Society, about a race of intelligent beings who predated humans. The fire trucks arriving to rescue Stevie have "Blackwood County" printed on the doors

The final scene takes place in Foum Tatouine, which is an actual place, used for filming the scenes on the planet Tatooine in Star Wars and Star Wars: Episode VI - Return of the Jedi.

In the original trailer, the shot with Mulder & Scully running from the bees was used, albeit minus the SFX bees.

After consuming much alcohol and finding the bar's bathroom locked, Mulder relieves himself on a movie poster for Independence Day. A line in Independence Day, spoken just after the first shot of the cable station, is "Yeah, I love X-Files too. I hardly get to see it."

Conrad Strughold (Armin Mueller-Stahl)was named for the real Strughold, a Nazi scientist who conducted experiments on prisoners during World War II.

Stevie is named after one of the original series creator Chris Carter's boyhood friends. Carter says that he and the real Stevie used to dig holes a lot, just like in the movie.

Former LAPD bomb squad officer Herb Williams and former FBI agent William O. Heaton acted as advisors for the bomb sequence - and appeared in the movie as agents in a scene with Scully.

The newspaper article Mulder reads at the end of the film (titled "Fatal Hanta Virus Outbreak in Northern Texas Reported Contained") was written by reporter Howard Dimsdale. The real Howard Dimsdale taught X-Files writers Frank Spotnitz and John Shiban at the American Film Institute, and was blacklisted during the McCarthy era, when he wrote under the name Arthur Dales, which was used as a name for the characters played in the series by Darren McGavin, M. Emmet Walsh and Fredric Lehne.

619 - the number on the "Office of Professional Review" door (where Scully is interrogated by the Assistant Directors). 06/19 is the date that the movie opened.

11:21 - the time Mulder goes to the Dallas Field Office, where Scully joins him and analyses the fossils. 11/21 is the birthdate of Chris Carter's wife.

Ten Thirteen Productions produced the film and the television series. On the last track of the movie soundtrack, if you let it play until 10:13, Chris Carter gives a description of some of the various conspiracies in the series and the movie. 10/13 is also the date in which the film came onto VHS in 1998.

In the chronology of the series, the movie takes place between the fifth season finale, "The End" (with the CSM torching Mulder's office) and the sixth season premiere "The Beginning" (which deals with the gestating-breed of aliens in the movie).

The scene in which Scully and Mulder are chased through a cornfield by helicopters is a reference to the famous "crop duster" scene in North by Northwest. Martin Landau was in both movies.

The video release has additional footage not shown in the theatrical release:

1. In the opening scene you now see more of the alien. In the theatrical release we see it fight off one of the cavemen, killing it, and the other caveman gets up to see it lying on the ground draining out the black blood (or what fans know as black oil). In the video release, we see it run off after it kills one of the cavemen, and when the other caveman gets up, he tracks it down and then kills it using the broken end of his torch.

2. In the scene with Mulder talking to the Well Manicured Man in the car, he reveals to Mulder that Samantha, Mulder's sister, was abducted by aliens at the request of her father, William Mulder, so she could be part of the colonization project, thus ensuring her survival in the colonization of Earth by the visitors. Also revealed is that when plans went awry, Mulder was intended, by his father, to seek the truth and reveal what had been done.

3. There is also an added scene in the video release with Mulder running down the street after the hospital scene.